You can replace the id for a class and initialise the players targeting the class name.

Example

Php/Html

while($row = mysql_fetch_assoc($query12))
{                               
    echo"<a  
    href='$urls'
    style='display:block;width:520px;height:330px' 
    class='player'> 
    </a> 
    <br/>                           
    <br/>";
}

JS

<script>
    flowplayer("a.player", {
    src:"flowplayer-3.2.16.swf",
    wmode: "opaque" // This allows the HTML to hide the flash content
    }, {
        clip: {
        autoPlay: false
       }
    });
</script>

This will now setup multiple players on your page.